﻿\begin{thebibliography}{0}

@article{zhang2006kaks_calculator,
  title={KaKs\_Calculator: calculating Ka and Ks through model selection and model averaging},
  author={Zhang, Zhang and Li, Jun and Zhao, Xiao-Qian and Wang, Jun and Wong, Gane Ka-Shu and Yu, Jun},
  journal={Genomics, Proteomics \& Bioinformatics},
  volume={4},
  number={4},
  pages={259--263},
  year={2006},
  publisher={Elsevier}
}

@article{moreno2008choosing,
  title={Choosing BLAST options for better detection of orthologs as reciprocal best hits},
  author={Moreno-Hagelsieb, Gabriel and Latimer, Kristen},
  journal={Bioinformatics},
  volume={24},
  number={3},
  pages={319--324},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{ning2001ssaha,
  title={SSAHA: a fast search method for large DNA databases},
  author={Ning, Zemin and Cox, Anthony J and Mullikin, James C},
  journal={Genome research},
  volume={11},
  number={10},
  pages={1725--1729},
  year={2001},
  publisher={Cold Spring Harbor Lab}
}

@article{thain2009chirp,
  title={Chirp: a practical global filesystem for cluster and Grid computing},
  author={Thain, Douglas and Moretti, Christopher and Hemmes, Jeffrey},
  journal={Journal of Grid Computing},
  volume={7},
  number={1},
  pages={51--72},
  year={2009},
  publisher={Springer}
}

@article{holm2010snpexp,
  title={SNPexp-A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels},
  author={Holm, Kristian and Melum, Espen and Franke, Andre and Karlsen, Tom H},
  journal={BMC bioinformatics},
  volume={11},
  number={1},
  pages={600},
  year={2010},
  publisher={BioMed Central Ltd}
}

@article{moreau2008special,
  title={Special issue: The first provenance challenge},
  author={Moreau, Luc and Lud{\"a}scher, Bertram and Altintas, Ilkay and Barga, Roger S and Bowers, Shawn and Callahan, Steven and Chin Jr, George and Clifford, Ben and Cohen, Shirley and Cohen-Boulakia, Sarah and others},
  journal={Concurrency and Computation: Practice and Experience},
  volume={20},
  number={5},
  pages={409--418},
  year={2008},
  publisher={Wiley Online Library}
}

@article{darling2003design,
  title={The design, implementation, and evaluation of mpiBLAST},
  author={Darling, Aaron and Carey, Lucas and Feng, Wu-chun},
  journal={Proceedings of ClusterWorld},
  volume={2003},
  year={2003}
}

@article{dumontier2002nblast,
  title={NBLAST: a cluster variant of BLAST for NxN comparisons},
  author={Dumontier, Michel and Hogue, Christopher},
  journal={BMC bioinformatics},
  volume={3},
  number={1},
  pages={13},
  year={2002},
  publisher={BioMed Central Ltd}
}

@article{tautz1984simple,
  title={Simple sequences are ubiquitous repetitive components of eukaryotic genomes},
  author={Tautz, Diethard and Renz, Manfred},
  journal={Nucleic Acids Research},
  volume={12},
  number={10},
  pages={4127--4138},
  year={1984},
  publisher={Oxford Univ Press}
}

@article{jeffreys1985hypervariable,
  title={Hypervariable‘minisatellite’ regions in human DNA},
  author={Jeffreys, Alec J and Wilson, Victoria and Thein, Swee Lay and others},
  journal={Nature},
  volume={314},
  number={6006},
  pages={67--73},
  year={1985},
  publisher={London}
}

@article{jeffreys1985individual,
  title={Individual-specific ‘fingerprints’ of human DNA},
  author={Jeffreys, AJ and Wilson, V and Thein, SL},
  journal={Nature},
  volume={316},
  number={6023},
  pages={76--79},
  year={1985}
}

@article{koressaar2007enhancements,
  title={Enhancements and modifications of primer design program Primer3},
  author={Koressaar, Triinu and Remm, Maido},
  journal={Bioinformatics},
  volume={23},
  number={10},
  pages={1289--1291},
  year={2007},
  publisher={Oxford Univ Press}
}

@article{nekrutenko2002ka,
  title={The KA/KS ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study},
  author={Nekrutenko, Anton and Makova, Kateryna D and Li, Wen-Hsiung},
  journal={Genome research},
  volume={12},
  number={1},
  pages={198--202},
  year={2002},
  publisher={Cold Spring Harbor Lab}
}

@phdthesis{fielding2000architectural,
  title={Architectural styles and the design of network-based software architectures},
  author={Fielding, Roy Thomas},
  year={2000},
  school={University of California}
}

@article{krasner1988description,
  title={A description of the model-view-controller user interface paradigm in the smalltalk-80 system},
  author={Krasner, Glenn E and Pope, Stephen T and others},
  journal={Journal of object oriented programming},
  volume={1},
  number={3},
  pages={26--49},
  year={1988}
}

@inproceedings{iseli1999estscan,
  title={ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences},
  author={Iseli, C. and Jongeneel, C.V. and Bucher, P. and others},
  booktitle={Proc Int Conf Intell Syst Mol Biol},
  volume={7},
  pages={138--148},
  year={1999}
}


@inproceedings{karo2001applying,
  title={Applying Grid technologies to bioinformatics},
  author={Karo, M. and Dwan, C. and Freeman, J. and Weissman, J. and Livny, M. and Retzel, E.},
  booktitle={High Performance Distributed Computing, 2001. Proceedings. 10th IEEE International Symposium on},
  pages={441--442},
  year={2001},
  organization={IEEE}
}


@article{taylor2010overview,
  title={An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics},
  author={Taylor, R.C.},
  journal={BMC bioinformatics},
  volume={11},
  number={Suppl 12},
  pages={S1},
  year={2010},
  publisher={BioMed Central Ltd}
}


@article{kryazhimskiy2008population,
  title={The population genetics of dN/dS},
  author={Kryazhimskiy, S. and Plotkin, J.B.},
  journal={PLoS genetics},
  volume={4},
  number={12},
  pages={e1000304},
  year={2008},
  publisher={Public Library of Science}
}


@article{aruliah2012best,
  title={Best Practices for Scientific Computing},
  author={Aruliah, DA and Brown, C.T. and Hong, N.P.C. and Davis, M. and Guy, R.T. and Haddock, S.H.D. and Huff, K. and Mitchell, I. and Plumbley, M. and Waugh, B. and others},
  journal={arXiv preprint arXiv:1210.0530},
  year={2012}
}

@inproceedings{litzkow1988condor,
  title={Condor-a hunter of idle workstations},
  author={Litzkow, Michael J and Livny, Miron and Mutka, Matt W},
  booktitle={Distributed Computing Systems, 1988., 8th International Conference on},
  pages={104--111},
  year={1988},
  organization={IEEE}
}

@article{carmichael2011biocompute,
  title={Biocompute 2.0: an improved collaborative workspace for data intensive bio-science},
  author={Carmichael, R. and Braga-Henebry, P. and Thain, D. and Emrich, S.},
  journal={Concurrency and Computation: Practice and Experience},
  volume={23},
  number={17},
  pages={2305--2314},
  year={2011},
  publisher={Wiley Online Library}
}

@inproceedings{albrecht2012makeflow,
  title={Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters, Clouds, and Grids},
  author={Albrecht, M. and Donnelly, P. and Bui, P. and Thain, D.},
  booktitle={Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET) at ACM SIGMOD},
  year={2012}
}

@article{feldman1979make,
  title={Make—A program for maintaining computer programs},
  author={Feldman, S.I.},
  journal={Software: Practice and experience},
  volume={9},
  number={4},
  pages={255--265},
  year={1979},
  publisher={Wiley Online Library}
}


@inproceedings{zhao2012designing,
  title={Designing and Deploying a Scientific Computing Cloud Platform},
  author={Zhao, Y. and Zhang, Y. and Tian, W. and Xue, R. and Lin, C.},
  booktitle={Grid Computing (GRID), 2012 ACM/IEEE 13th International Conference on},
  pages={104--113},
  year={2012},
  organization={IEEE}
}


@inproceedings{gonzalez2007web,
  title={Web service orchestration for bioinformatics systems: challenges and current workflow definition approaches},
  author={Gonzalez, G. and Balasooriya, J.},
  booktitle={Web Services, 2007. ICWS 2007. IEEE International Conference on},
  pages={1226--1227},
  year={2007},
  organization={IEEE}
}


@article{orvis2010ergatis,
  title={Ergatis: a web interface and scalable software system for bioinformatics workflows},
  author={Orvis, J. and Crabtree, J. and Galens, K. and Gussman, A. and Inman, J.M. and Lee, E. and Nampally, S. and Riley, D. and Sundaram, J.P. and Felix, V. and others},
  journal={Bioinformatics},
  volume={26},
  number={12},
  pages={1488--1492},
  year={2010},
  publisher={Oxford Univ Press}
}

@misc{phobos,
  author = {Mayer, C.},
  title = {Phobos 3.3.11},
  year = {2006}, 
  url = {http://www.rub.de/spezzoo/cm/cm_phobos.htm}
}

@misc{sputnik,
  author = {Abajian, C.},
  title = {SPUTNIK},
  title={Codon catalog usage and the genome hypothesis},
  author={Grantham, R. and Gautier, C. and Gouy, M. and Mercier, R. and Pave, A.},
  journal={Nucleic acids research},
  volume={8},
  number={1},
  pages={197--197},
  year={1980},
  publisher={Oxford Univ Press}
}


@article{duret2002evolution,
  title={Evolution of synonymous codon usage in metazoans},
  author={Duret, L.},
  journal={Current opinion in genetics \& development},
  volume={12},
  number={6},
  pages={640--649},
  year={2002},
  publisher={Elsevier}
}


@article{smith2001translationally,
  title={Why are translationally sub-optimal synonymous codons used in Escherichia coli?},
  author={Smith, N.G.C. and Eyre-Walker, A.},
  journal={Journal of Molecular Evolution},
  volume={53},
  number={3},
  pages={225--236},
  year={2001},
  publisher={Springer}
}


@article{clarke2008rare,
  title={Rare codons cluster},
  author={Clarke, T.F. and Clark, P.L.},
  journal={PLoS One},
  volume={3},
  number={10},
  pages={e3412},
  year={2008},
  publisher={Public Library of Science}
}


@article{li2003orthomcl,
  title={OrthoMCL: identification of ortholog groups for eukaryotic genomes},
  author={Li, L. and Stoeckert, C.J. and Roos, D.S.},
  journal={Genome research},
  volume={13},
  number={9},
  pages={2178--2189},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}


@article{rice2000emboss,
  title={EMBOSS: the European molecular biology open software suite},
  author={Rice, P. and Longden, I. and Bleasby, A. and others},
  journal={Trends in genetics},
  volume={16},
  number={6},
  pages={276--277},
  year={2000},
  publisher={[Amsterdam, The Netherlands: Elsevier Science Publishers (Biomedical Division)], c1985-}
}


@article{edgar2004muscle,
  title={MUSCLE: multiple sequence alignment with high accuracy and high throughput},
  author={Edgar, R.C.},
  journal={Nucleic acids research},
  volume={32},
  number={5},
  pages={1792--1797},
  year={2004},
  publisher={Oxford Univ Press}
}


@article{miller2008aggressive,
  title={Aggressive assembly of pyrosequencing reads with mates},
  author={Miller, J.R. and Delcher, A.L. and Koren, S. and Venter, E. and Walenz, B.P. and Brownley, A. and Johnson, J. and Li, K. and Mobarry, C. and Sutton, G.},
  journal={Bioinformatics},
  volume={24},
  number={24},
  pages={2818--2824},
  year={2008},
  publisher={Oxford Univ Press}
}


@inproceedings{thrasher2010taming,
  title={Taming complex bioinformatics workflows with Weaver, Makeflow, and Starch},
  author={Thrasher, A. and Carmichael, R. and Bui, P. and Yu, L. and Thain, D. and Emrich, S.},
  booktitle={Workflows in Support of Large-Scale Science (WORKS), 2010 5th Workshop on},
  pages={1--6},
  year={2010},
  organization={IEEE}
}


@inproceedings{yu2012resource,
  title={Resource Management for Elastic Cloud Workflows},
  author={Yu, L. and Thain, D.},
  booktitle={Proceedings of the 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012)},
  pages={775--780},
  year={2012},
  organization={IEEE Computer Society}
}
@article{lawson2007vectorbase,
  title={VectorBase: a home for invertebrate vectors of human pathogens},
  author={Lawson, Daniel and Arensburger, Peter and Atkinson, Peter and Besansky, Nora J and Bruggner, Robert V and Butler, Ryan and Campbell, Kathryn S and Christophides, George K and Christley, Scott and Dialynas, Emmanuel and others},
  journal={Nucleic Acids Research},
  volume={35},
  number={suppl 1},
  pages={D503--D505},
  year={2007},
  publisher={Oxford Univ Press}
}

@article{johnson2008ncbi,
  title={NCBI BLAST: a better web interface},
  author={Johnson, Mark and Zaretskaya, Irena and Raytselis, Yan and Merezhuk, Yuri and McGinnis, Scott and Madden, Thomas L},
  journal={Nucleic acids research},
  volume={36},
  number={suppl 2},
  pages={W5--W9},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{grantham1980codon,
  title={Codon catalog usage and the genome hypothesis},
  author={Grantham, R and Gautier, C and Gouy, M and Mercier, R and Pave, A},
  journal={Nucleic acids research},
  volume={8},
  number={1},
  pages={197--197},
  year={1980},
  publisher={Oxford Univ Press}
}

@article{chartier2012large,
  title={Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events},
  author={Chartier, M. and Gaudreault, F. and Najmanovich, R.},
  journal={Bioinformatics},
  volume={28},
  number={11},
  pages={1438--1445},
  year={2012},
  publisher={Oxford Univ Press}
}


@article{zhang2012codon,
  title={Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance},
  author={Zhang, Z. and Li, J. and Cui, P. and Ding, F. and Li, A. and Townsend, J.P. and Yu, J.},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={43},
  year={2012},
  publisher={BioMed Central Ltd}
}


#Transcriptome Analysis Citations
@article{lazzari2008version,
  title={Version VI of the ESTree db: an improved tool for peach transcriptome analysis},
  author={Lazzari, B. and Caprera, A. and Vecchietti, A. and Merelli, I. and Barale, F. and Milanesi, L. and Stella, A. and Pozzi, C.},
  journal={BMC bioinformatics},
  volume={9},
  number={Suppl 2},
  pages={S9},
  year={2008},
  publisher={BioMed Central Ltd}
}


@article{bateman2004pfam,
  title={The Pfam protein families database},
  author={Bateman, A. and Coin, L. and Durbin, R. and Finn, R.D. and Hollich, V. and Griffiths-Jones, S. and Khanna, A. and Marshall, M. and Moxon, S. and Sonnhammer, E.L.L. and others},
  journal={Nucleic acids research},
  volume={32},
  number={suppl 1},
  pages={D138--D141},
  year={2004},
  publisher={Oxford Univ Press}
}


@article{eddy2011accelerated,
  title={Accelerated profile HMM searches},
  author={Eddy, S.R.},
  journal={PLoS Computational Biology},
  volume={7},
  number={10},
  pages={e1002195},
  year={2011},
  publisher={Public Library of Science}
}


\end{thebibliography}\end{document}
